基于FPGA的分子动力学模拟系统设计

FPGA-Based Molecular Dynamics Simulations System Design

FPGA加速分子动力学模拟在材料科学、分子科学等方面应用广泛,一直是高性能计算领域的热门话题之一.在分子动力学模拟中,分子间作用力(LJ力)的计算是整个过程耗时最长的部分,文中设计的系统将其放在FP-GA上完成,其余部分由CPU完成.根据LJ力的特点,FPGA加速的计算采用以下方法进行设计:利用邻近粒子搜索算法-元胞列表算法选取粒子对,并使用过滤模块进一步减少计算量;计算LJ力时采用先离散后插值的方法计算公式中的高次幂同时避免了开方运算.所有部件组成流水线结构,进一步提高整体的性能.

FPGA-based acceleration of Molecular Dynamics （MD） simulation, which is widely used in many fields from materials science to molecular science, has been the subject of high performance studies. The force calculations consume long time in the whole system. In this paper, we propose a system that can implement the Lennard-Jones （LJ） force computation on FPGA, and the remaining computations are computed by the host. According to the property of LJ force, we use the following methods： cell-list method, combining discrete function and interpolation for computing high power to avoid square root operation. All units organize as a pipeline to improve the performance of the system.